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PLoS Genetics

Chao Zhang, Yi Shen, Ding Tang, Wenqing Shi, Dongmei Zhang, Guijie Du, Yihua Zhou, Guohua Liang, Yafei Li, Zhukuan Cheng
Meiotic cytokinesis influences the fertility and ploidy of gametes. However, limited information is available on the genetic control of meiotic cytokinesis in plants. Here, we identified a rice mutant with low male fertility, defective callose in meiosis 1 (dcm1). The pollen grains of dcm1 are proved to be defective in exine formation. Meiotic cytokinesis is disrupted in dcm1, resulting in disordered spindle orientation during meiosis II and formation of pollen grains with varied size and DNA content. We demonstrated that meiotic cytokinesis defect in dcm1 is caused by prematurely dissolution of callosic plates...
November 12, 2018: PLoS Genetics
Magali Jaillard, Leandro Lima, Maud Tournoud, Pierre Mahé, Alex van Belkum, Vincent Lacroix, Laurent Jacob
Genome-wide association study (GWAS) methods applied to bacterial genomes have shown promising results for genetic marker discovery or detailed assessment of marker effect. Recently, alignment-free methods based on k-mer composition have proven their ability to explore the accessory genome. However, they lead to redundant descriptions and results which are sometimes hard to interpret. Here we introduce DBGWAS, an extended k-mer-based GWAS method producing interpretable genetic variants associated with distinct phenotypes...
November 12, 2018: PLoS Genetics
Lusine Nazaryan-Petersen, Jesper Eisfeldt, Maria Pettersson, Johanna Lundin, Daniel Nilsson, Josephine Wincent, Agne Lieden, Lovisa Lovmar, Jesper Ottosson, Jelena Gacic, Outi Mäkitie, Ann Nordgren, Francesco Vezzi, Valtteri Wirta, Max Käller, Tina Duelund Hjortshøj, Cathrine Jespersgaard, Rayan Houssari, Laura Pignata, Mads Bak, Niels Tommerup, Elisabeth Syk Lundberg, Zeynep Tümer, Anna Lindstrand
Clustered copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) are often reported as germline chromothripsis. However, such cases might need further investigations by massive parallel whole genome sequencing (WGS) in order to accurately define the underlying complex rearrangement, predict the occurrence mechanisms and identify additional complexities. Here, we utilized WGS to delineate the rearrangement structure of 21 clustered CNV carriers first investigated by CMA and identified a total of 83 breakpoint junctions (BPJs)...
November 12, 2018: PLoS Genetics
Caitlin Morris, Olivia K Foster, Simran Handa, Kimberly Peloza, Laura Voss, Hannah Somhegyi, Youli Jian, My Van Vo, Marie Harp, Fiona M Rambo, Chonglin Yang, Greg J Hermann
Cell type-specific modifications of conventional endosomal trafficking pathways lead to the formation of lysosome-related organelles (LROs). C. elegans gut granules are intestinally restricted LROs that coexist with conventional degradative lysosomes. The formation of gut granules requires the Rab32 family member GLO-1. We show that the loss of glo-1 leads to the mistrafficking of gut granule proteins but does not significantly alter conventional endolysosome biogenesis. GLO-3 directly binds to CCZ-1 and they both function to promote the gut granule association of GLO-1, strongly suggesting that together, GLO-3 and CCZ-1 activate GLO-1...
November 12, 2018: PLoS Genetics
Vamsi K Gali, David Dickerson, Yuki Katou, Katsunori Fujiki, Katsuhiko Shirahige, Tom Owen-Hughes, Takashi Kubota, Anne D Donaldson
Elg1, the major subunit of a Replication Factor C-like complex, is critical to ensure genomic stability during DNA replication, and is implicated in controlling chromatin structure. We investigated the consequences of Elg1 loss for the dynamics of chromatin re-formation following DNA replication. Measurement of Okazaki fragment length and the micrococcal nuclease sensitivity of newly replicated DNA revealed a defect in nucleosome organization in the absence of Elg1. Using a proteomic approach to identify Elg1 binding partners, we discovered that Elg1 interacts with Rtt106, a histone chaperone implicated in replication-coupled nucleosome assembly that also regulates transcription...
November 12, 2018: PLoS Genetics
Yaxian Lan, Xiaonan Liu, Ying Fu, Shanjin Huang
A population of dynamic apical actin filaments is required for rapid polarized pollen tube growth. However, the cellular mechanisms driving their assembly remain incompletely understood. It was postulated that formin is a major player in nucleating apical actin assembly, but direct genetic and cytological evidence remains to be firmly established. Here we found that both Arabidopsis formin 3 (AtFH3) and formin 5 (AtFH5) are involved in the regulation of apical actin polymerization and actin array construction in pollen tubes, with AtFH3 playing a more dominant role...
November 12, 2018: PLoS Genetics
Nhung H Vuong, David P Cook, Laura A Forrest, Lauren E Carter, Pascale Robineau-Charette, Joshua M Kofsky, Kendra M Hodgkinson, Barbara C Vanderhyden
Estrogen therapy increases the risk of ovarian cancer and exogenous estradiol accelerates the onset of ovarian cancer in mouse models. Both in vivo and in vitro, ovarian surface epithelial (OSE) cells exposed to estradiol develop a subpopulation that loses cell polarity, contact inhibition, and forms multi-layered foci of dysplastic cells with increased susceptibility to transformation. Here, we use single-cell RNA-sequencing to characterize this dysplastic subpopulation and identify the transcriptional dynamics involved in its emergence...
November 12, 2018: PLoS Genetics
Rebecca C Poulos, Yuen T Wong, Regina Ryan, Herbert Pang, Jason W H Wong
Driver mutations are the genetic variants responsible for oncogenesis, but how specific somatic mutational events arise in cells remains poorly understood. Mutational signatures derive from the frequency of mutated trinucleotides in a given cancer sample, and they provide an avenue for investigating the underlying mutational processes that operate in cancer. Here we analyse somatic mutations from 7,815 cancer exomes from The Cancer Genome Atlas (TCGA) across 26 cancer types. We curate a list of 50 known cancer driver mutations by analysing recurrence in our cohort and annotations of known cancer-associated genes from the Cancer Gene Census, IntOGen database and Cancer Genome Interpreter...
November 9, 2018: PLoS Genetics
Fernando H Ramírez-Guadiana, Christopher D A Rodrigues, Kathleen A Marquis, Nathalie Campo, Rocío Del Carmen Barajas-Ornelas, Kelly Brock, Debora S Marks, Andrew C Kruse, David Z Rudner
During the morphological process of sporulation in Bacillus subtilis two adjacent daughter cells (called the mother cell and forespore) follow different programs of gene expression that are linked to each other by signal transduction pathways. At a late stage in development, a signaling pathway emanating from the forespore triggers the proteolytic activation of the mother cell transcription factor σK. Cleavage of pro-σK to its mature and active form is catalyzed by the intramembrane cleaving metalloprotease SpoIVFB (B), a Site-2 Protease (S2P) family member...
November 7, 2018: PLoS Genetics
François Rousset, Lun Cui, Elise Siouve, Christophe Becavin, Florence Depardieu, David Bikard
High-throughput genetic screens are powerful methods to identify genes linked to a given phenotype. The catalytic null mutant of the Cas9 RNA-guided nuclease (dCas9) can be conveniently used to silence genes of interest in a method also known as CRISPRi. Here, we report a genome-wide CRISPR-dCas9 screen using a starting pool of ~ 92,000 sgRNAs which target random positions in the chromosome of E. coli. To benchmark our method, we first investigate its utility to predict gene essentiality in the genome of E...
November 7, 2018: PLoS Genetics
Daniela Pignatta, Katherine Novitzky, P R V Satyaki, Mary Gehring
The contribution of epigenetic variation to phenotypic variation is unclear. Imprinted genes, because of their strong association with epigenetic modifications, represent an opportunity for the discovery of such phenomena. In mammals and flowering plants, a subset of genes are expressed from only one parental allele in a process called gene imprinting. Imprinting is associated with differential DNA methylation and chromatin modifications between parental alleles. In flowering plants imprinting occurs in a seed tissue-endosperm...
November 5, 2018: PLoS Genetics
Shuang Li, Daniella M Giardina, Mark L Siegal
Genetically identical cells exhibit extensive phenotypic variation even under constant and benign conditions. This so-called nongenetic heterogeneity has important clinical implications: within tumors and microbial infections, cells show nongenetic heterogeneity in growth rate and in susceptibility to drugs or stress. The budding yeast, Saccharomyces cerevisiae, shows a similar form of nongenetic heterogeneity in which growth rate correlates positively with susceptibility to acute heat stress at the single-cell level...
November 2, 2018: PLoS Genetics
Roger C Ma, Craig T Jacobs, Priyanka Sharma, Katrinka M Kocha, Peng Huang
Development of a functional musculoskeletal system requires coordinated generation of muscles, bones, and tendons. However, how axial tendon cells (tenocytes) are generated during embryo development is still poorly understood. Here, we show that axial tenocytes arise from the sclerotome in zebrafish. In contrast to mouse and chick, the zebrafish sclerotome consists of two separate domains: a ventral domain and a previously undescribed dorsal domain. While dispensable for sclerotome induction, Hedgehog (Hh) signaling is required for the migration and maintenance of sclerotome derived cells...
November 2, 2018: PLoS Genetics
Eduardo G Dupim, Gabriel Goldstein, Thyago Vanderlinde, Suzana C Vaz, Flávia Krsticevic, Aline Bastos, Thadeo Pinhão, Marcos Torres, Jean R David, Carlos R Vilela, Antonio Bernardo Carvalho
Y chromosomes are widely believed to evolve from a normal autosome through a process of massive gene loss (with preservation of some male genes), shaped by sex-antagonistic selection and complemented by occasional gains of male-related genes. The net result of these processes is a male-specialized chromosome. This might be expected to be an irreversible process, but it was found in 2005 that the Drosophila pseudoobscura Y chromosome was incorporated into an autosome. Y chromosome incorporations have important consequences: a formerly male-restricted chromosome reverts to autosomal inheritance, and the species may shift from an XY/XX to X0/XX sex-chromosome system...
November 2, 2018: PLoS Genetics
Yang Liu, Qianchan He, Wei Sun
Somatic mutations drive the growth of tumor cells and are pivotal biomarkers for many cancer treatments. Genetic association analysis using somatic mutations is an effective approach to study the functional impact of somatic mutations. However, standard regression methods are not appropriate for somatic mutation association studies because somatic mutation calls often have non-ignorable false positive rate and/or false negative rate. While large scale association analysis using somatic mutations becomes feasible recently-thanks for the improvement of sequencing techniques and the reduction of sequencing cost-there is an urgent need for a new statistical method designed for somatic mutation association analysis...
November 2, 2018: PLoS Genetics
Nisha Rathore, Sree Ranjani Ramani, Homer Pantua, Jian Payandeh, Tushar Bhangale, Arthur Wuster, Manav Kapoor, Yonglian Sun, Sharookh B Kapadia, Lino Gonzalez, Ali A Zarrin, Alison Goate, David V Hansen, Timothy W Behrens, Robert R Graham
Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA) is a cell surface inhibitory receptor that recognizes specific O-glycosylated proteins and is expressed on various innate immune cell types including microglia. We show here that a common missense variant (G78R, rs1859788) of PILRA is the likely causal allele for the confirmed Alzheimer's disease risk locus at 7q21 (rs1476679). The G78R variant alters the interaction of residues essential for sialic acid engagement, resulting in >50% reduced binding for several PILRA ligands including a novel ligand, complement component 4A, and herpes simplex virus 1 (HSV-1) glycoprotein B...
November 2, 2018: PLoS Genetics
Hanh Nguyen, Sara Labella, Nicola Silva, Verena Jantsch, Monique Zetka
Correct segregation of meiotic chromosomes depends on DNA crossovers (COs) between homologs that culminate into visible physical linkages called chiasmata. COs emerge from a larger population of joint molecules (JM), the remainder of which are repaired as noncrossovers (NCOs) to restore genomic integrity. We present evidence that the RNF212-like C. elegans protein ZHP-4 cooperates with its paralog ZHP-3 to enforce crossover formation at distinct steps during meiotic prophase: in the formation of early JMs and in transition of late CO intermediates into chiasmata...
October 31, 2018: PLoS Genetics
Lianna R Walker, Taylor B Engle, Hiep Vu, Emily R Tosky, Dan J Nonneman, Timothy P L Smith, Tudor Borza, Thomas E Burkey, Graham S Plastow, Stephen D Kachman, Daniel C Ciobanu
Porcine circovirus 2 (PCV2) is a circular single-stranded DNA virus responsible for a group of diseases collectively known as PCV2 Associated Diseases (PCVAD). Variation in the incidence and severity of PCVAD exists between pigs suggesting a host genetic component involved in pathogenesis. A large-scale genome-wide association study of experimentally infected pigs (n = 974), provided evidence of a host genetic role in PCV2 viremia, immune response and growth during challenge. Host genotype explained 64% of the phenotypic variation for overall viral load, with two major Quantitative Trait Loci (QTL) identified on chromosome 7 (SSC7) near the swine leukocyte antigen complex class II locus and on the proximal end of chromosome 12 (SSC12)...
October 31, 2018: PLoS Genetics
Mikkel-Holger S Sinding, Shyam Gopalakrishan, Filipe G Vieira, Jose A Samaniego Castruita, Katrine Raundrup, Mads Peter Heide Jørgensen, Morten Meldgaard, Bent Petersen, Thomas Sicheritz-Ponten, Johan Brus Mikkelsen, Ulf Marquard-Petersen, Rune Dietz, Christian Sonne, Love Dalén, Lutz Bachmann, Øystein Wiig, Anders J Hansen, M Thomas P Gilbert
North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0...
November 2018: PLoS Genetics
Pritesh Krishnakumar, Stephan Riemer, Roshan Perera, Thomas Lingner, Alexander Goloborodko, Hazem Khalifa, Franck Bontems, Felix Kaufholz, Mohamed A El-Brolosy, Roland Dosch
The proteins Oskar (Osk) in Drosophila and Bucky ball (Buc) in zebrafish act as germ plasm organizers. Both proteins recapitulate germ plasm activities but seem to be unique to their animal groups. Here, we discover that Osk and Buc show similar activities during germ cell specification. Drosophila Osk induces additional PGCs in zebrafish. Surprisingly, Osk and Buc do not show homologous protein motifs that would explain their related function. Nonetheless, we detect that both proteins contain stretches of intrinsically disordered regions (IDRs), which seem to be involved in protein aggregation...
November 2018: PLoS Genetics
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